The cause of this issue is in eZCollaborationItemHandler::fetchList in kernel/classes/ezcollaborationitemhandler.php

It can be fixed by changing line 589

$list[] =& $handlerInstance;

to

$list[] = $handlerInstance;

You can see what's happening looking at the code

foreach ( $activeHandlers as $handler )
{
   $handlerInstance = eZCollaborationItemHandler::instantiate( $handler, $repositories );
   if ( $handlerInstance !== null )
       $list[] =& $handlerInstance;
}

The reference to $handlerInstance is being appended to the list array. When there are multiple handlers the reference is updated with the values returned from eZCollaborationItemHandler::instantiate. "list" becomes an array of references to the last valid handler instance.

Steps to reproduce

Add an additional workflow that contains a collaboration handler. e.g. eZApprove2 http://projects.ez.no/ezapprove2

Assuming the extension is activated visiting My Account -> My notification settings will show the last Collaboration notification item repeated.